diff --git a/src/nf_modules/stringtie/transcriptome_longReads.config b/src/nf_modules/stringtie/transcriptome_longReads.config
new file mode 100644
index 0000000000000000000000000000000000000000..1a385c7ec2be80c7a7af4424ab7d2b629ba6c600
--- /dev/null
+++ b/src/nf_modules/stringtie/transcriptome_longReads.config
@@ -0,0 +1,12 @@
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: stringtie {
+        cpus = 1
+        container = "informationsea/stringtie:2.1.1"
+      }
+    }
+  }
+}
diff --git a/src/nf_modules/stringtie/transcriptome_longReads.nf b/src/nf_modules/stringtie/transcriptome_longReads.nf
new file mode 100644
index 0000000000000000000000000000000000000000..e0ba8bd2406d726968f6af9d619a7112b55873b3
--- /dev/null
+++ b/src/nf_modules/stringtie/transcriptome_longReads.nf
@@ -0,0 +1,33 @@
+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+
+///////////////////////////////////////////////////////////////////////////////
+// TRANSCRIPTOME BUILDING
+
+process stringtie {
+  tag "$file_id"
+  publishDir "results/stringtie/${file_id}", mode: 'copy'
+
+ input:
+ set file_id, file(bam) from bam_files
+
+ output:
+ file "*.gtf" into gtf_transcriptome
+
+ script:
+ """
+stringtie -L \
+          -o ${file_id}.gtf \
+          -f 0.001 \
+          -j 0.5 ${bam}
+ """
+}
+
+// END STRNGTIE
diff --git a/src/nf_modules/stringtie/transcriptome_shortReads.nf b/src/nf_modules/stringtie/transcriptome_shortReads.nf
new file mode 100644
index 0000000000000000000000000000000000000000..68ad9999367132d4326c061b1ed434f07f863def
--- /dev/null
+++ b/src/nf_modules/stringtie/transcriptome_shortReads.nf
@@ -0,0 +1,32 @@
+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+
+///////////////////////////////////////////////////////////////////////////////
+// TRANSCRIPTOME BUILDING
+
+process stringtie {
+  tag "$file_id"
+  publishDir "results/stringtie/${file_id}", mode: 'copy'
+
+ input:
+ set file_id, file(bam) from bam_files
+
+ output:
+ file "*.gtf" into gtf_files
+
+ script:
+ """
+stringtie -o ${file_id}.gtf \
+          -f 0.01 \
+          -j 0.5 ${bam}
+ """
+}
+
+// END STRNGTIE